package main;

import io.GeneFileReader;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;

import util.Extractor;
import util.Gene;

public class Main {

	/**
	 * @param args
	 * @throws IOException 
	 * @throws FileNotFoundException 
	 */
	public static void main(String[] args) throws FileNotFoundException, IOException {
	
		//Aquifex aeolicus.ffn 1
		//Archaeoglobus fulgidus.ffn 2
		//Bacillus subtilis.ffn 3
		//Bacteroides thetaiotaomicron.ffn 4
		//Chlamydia muridarum.ffn 5
		//Dehalococcoides ethenogenes.ffn 6
		//Escherichia coli.ffn 7
		//Fusobacterium nucleatum.ffn 8
		//Gloeobacter violaceus.ffn 9
		//Leptospira interrogans.ffn 10
		//Nanoarchaeum equitans.ffn 11
		//Pirellula.ffn 12
		//Rubrobacter xylanophilus.ffn 13
		//Sulfolobus acidocaldarius.ffn 14
		//Thermotoga maritima.ffn 15
		//Thermus thermophilus.ffn 16
		
		String organism = "Thermus thermophilus.ffn";
		GeneFileReader gfr = new GeneFileReader(new FileInputStream(new File(
				"organisms/" + organism)));
		//System.out.println("number of genes:"+gfr.numberOfGenes());
		/*System.out.println(gfr.getAnnotationAt(1));
		System.out.println(gfr.getGeneAt(1));
		System.out.println(gfr.getAnnotationAt(1257));
		System.out.println(gfr.getGeneAt(1257));*/
		
		Extractor e=new Extractor(gfr);
		e.extract();
		
		


	}

}
